Purpose To describe a novel alternative technique for C2 fixation under the concept of atlantoaxial joint distraction and fusion with intra-articular Cages, and to report its preliminary clinical outcomes. Methods Eighteen patients with basilar invagination and atlantoaxial dislocation underwent atlantoaxial joint distraction and fusion with intra-articular Cages. All patients had hypoplasia of the C2 isthmus prohibiting insertion of the pedicle screw. A new method, the C2 anatomical pedicle screw (C2APS) was used as an alternative. In this technique, we directly inserted screw into the C2 anatomical pedicle after facet joint distraction and Cage implementation. The trajectory mostly went through the anatomical pedicle, which completely bypasses the variated VA and decreases the risk of VA harm. The dense anatomical pedicle could provide robust and secure screw purchase. Results C2APS was indicated for 32 screws in 18 patients. Satisfactory C2APS placement was achieved in all patients. No VA injury was observed. Sufficient reduction and decompression were achieved in all cases. There were no cases of implant failure, and all patients demonstrated solid fusion. JOA scores improved from 14.6 +/- 1.5 preoperatively, to 16.0 +/- 0.8 at the final follow-up (p < 0.01). The measured radiographic indices for basilar invagination and atlantoaxial dislocation significantly improved. Conclusion This novel technique can provide reliable fixation of the axis while eliminating VA injury. When placement of a C2 pedicle screw is not possible due to anatomical constraints, C2APS can be considered as a safe and efficient alternative when the technique of atlantoaxial joint distraction and fusion with intra-articular Cages was used.